# 2D

2D is a numerical Hartree-Fock program for diatomic molecules.

# "Understanding Molecular Simulations"

The FORTRAN source code of the Case Studies of the book Understanding Molecular Simulations.

# ABINIT

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation).

# ADF

ADF is the Amsterdam Density Functional program system for high-quality computational chemistry research. The two main programs are ADF, for molecules, and BAND for periodic structures: polymers, slabs, and crystals. Several smaller utility and property programs are available for pre- and post-processing data of the main calculations.

# Almond

ALMOND is a program specifically developed for generating and handling alignment independent descriptors called GRIND (GRid INdependent Descriptors). These are a new generation of 3D-molecular descriptors with application in 3D-QSAR, QSAR, virtual screening, design of combinatorial libraries, selectivity studies and in any field where 3D quantitative pharmacophoric description for (macro)molecules is needed.

# ALOGPS

ALOGPS provides prediction of logP and aqueous solubility of compounds to be used in drug design (ADMET and HTS) and environmental chemistry studies. The ALOGPS program can be also used to predict logD values.

# AmberFFC

AmberFFC is designed to convert the different existing AMBER force fields (FF) freely available in the public domain, for use with commercial molecular modeling packages, using the MSI software package as a case model.

# AMMP

AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. In addition to standard features, like numerically stable molecular dynamics, fast multipole method for including all atoms in the calculation of long range potentials and robust structural optimizers, it has a flexible choice of potentials and a simple yet powerful ability to manipulate molecules and analyze individual energy terms.

# AMPAC with GUI

AMPAC is a fully-featured semiempirical QM program. It also includes a graphical user interface (GUI) that builds molecules and offers full visualization of results.

# AQUA

AQUA is a suite of programs for Analyzing the QUAlity of biomolecular structures that were determined via NMR spectroscopy. AQUA is capable of calculating NOE violations, the level of completeness of NOEs based on the structure.